BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0029.0288.p (385 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription... 775 0.0 gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcriptio... 251 1e-67 gi|300313916|ref|YP_003778008.1| two component response regulato... 208 6e-55 gi|300312042|ref|YP_003776134.1| response regulatory protein [He... 202 3e-53 gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip... 197 1e-51 >gi|300313101|ref|YP_003777193.1| sigma54-dependent transcription regulator protein [Herbaspirillum seropedicae SmR1] Length = 437 Score = 775 bits (2002), Expect = 0.0, Method: Compositional matrix adjust. Identities = 382/385 (99%), Positives = 383/385 (99%) Query: 1 MPTTPVEQPLAEAEADSDVRTSTAARSASSRHAPRYRDIDQLAAGDACMHDLVERGKRLI 60 MPTTPVEQPLAEAEADSDVRTSTAARSASSRHAPRYRDIDQLAAGDACMHDL+ERGKRLI Sbjct: 53 MPTTPVEQPLAEAEADSDVRTSTAARSASSRHAPRYRDIDQLAAGDACMHDLIERGKRLI 112 Query: 61 DRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPESLAESELFGYCKGAFS 120 DRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPESLAESELFGYCKGAFS Sbjct: 113 DRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPESLAESELFGYCKGAFS 172 Query: 121 GALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVIPLGARHPVPVDVQLI 180 GALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVIPLGARHPVPVDVQLI Sbjct: 173 GALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVIPLGARHPVPVDVQLI 232 Query: 181 CATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRERSDRRRLVMQMITEELGRSADDSV 240 CATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRERSDRRRLVMQMITEELGR ADDSV Sbjct: 233 CATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRERSDRRRLVMQMITEELGRPADDSV 292 Query: 241 IEAAALQRLLAYPWPGNLRQMHAVIRYSCAVMNGGRIEVRDLPEELMQFQPATLAEVHPI 300 IEAAALQRLLAYPWPGNLRQMHAVIRYSCAVMNGGRIEVRDLPEELMQFQPATLAEVHPI Sbjct: 293 IEAAALQRLLAYPWPGNLRQMHAVIRYSCAVMNGGRIEVRDLPEELMQFQPATLAEVHPI 352 Query: 301 TRTAQIRPFTSRAEGEAGRERSSGDPYRDERTRVIDALNGSRWNISAASRQLGMCRASLY 360 TRTAQIRPFTSRAEGEAGRERSSGDPYRDERTRVIDALNGSRWNISAASRQLGMCRASLY Sbjct: 353 TRTAQIRPFTSRAEGEAGRERSSGDPYRDERTRVIDALNGSRWNISAASRQLGMCRASLY 412 Query: 361 RKLRQLDIPHVRDQAMPAYPTYAVA 385 RKLRQLDIPHVRDQAMPAYP YAVA Sbjct: 413 RKLRQLDIPHVRDQAMPAYPAYAVA 437 >gi|300311223|ref|YP_003775315.1| sigma-54 dependent transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 675 Score = 251 bits (640), Expect = 1e-67, Method: Compositional matrix adjust. Identities = 150/337 (44%), Positives = 207/337 (61%), Gaps = 26/337 (7%) Query: 38 DIDQLAAGDACMHDLVERGKRLIDRGIPVLILGETGTGKEYLSRALHDYSARR------- 90 D+ L GD M ++ + +R+IDR IP+LI GETGTGKE+L++A+H SAR Sbjct: 351 DLQALDTGDVRMSAIIAKLRRVIDRDIPILITGETGTGKEWLAQAIHGDSARFGARQNRA 410 Query: 91 -RASWIAVNCASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPL 149 A ++AVNC++IPE+L E+ELFGY GAF+GA G GK+ QA GGTLFLDEIGDMPL Sbjct: 411 GAAPFVAVNCSAIPENLIEAELFGYEDGAFTGARRKGALGKIAQAHGGTLFLDEIGDMPL 470 Query: 150 ALQTRLLRVLSEREVIPLGARHPVPVDVQLICATHQDLKTLIAEGRFREDLYYRVAGGVL 209 ALQ RLLRVL ER V PLG++ +PVD L+CAT+Q L+ + A FREDLYYR+ G + Sbjct: 471 ALQGRLLRVLQERAVTPLGSQRVIPVDFALVCATNQPLREMAARHAFREDLYYRINGLQV 530 Query: 210 RLPALRERSDRRRLVMQMITEELGRSADDSVIEAAALQRLLAYPWPGNLRQMHAVIRYSC 269 +LPALR+RSD +L+ +++ +E G A +A AL LLA WPGNLRQ+ ++R S Sbjct: 531 KLPALRDRSDLPQLIERILEDEGGPHAPRFDAQAQAL--LLASHWPGNLRQLANLVRTSL 588 Query: 270 AVMNGGR-IEVRDLPEELMQFQPATLAEVHPITRTAQIRPFTSRAEGEAGRERSSGDPYR 328 A+ G I LP++ ++ + +H T RS + Sbjct: 589 AMAEGEEAIGPHHLPDDFLE-EAGAPGALHDGMHTMHA-------------VRSDCLSIQ 634 Query: 329 DERTRVID-ALNGSRWNISAASRQLGMCRASLYRKLR 364 D I+ AL N+SAA++ LG+ R ++YR+L+ Sbjct: 635 DNEWAAIERALRTHAGNVSAAAKALGVSRNTIYRRLK 671 >gi|300313916|ref|YP_003778008.1| two component response regulator protein [Herbaspirillum seropedicae SmR1] Length = 448 Score = 208 bits (530), Expect = 6e-55, Method: Compositional matrix adjust. Identities = 136/331 (41%), Positives = 185/331 (55%), Gaps = 17/331 (5%) Query: 40 DQLAAGDACMHDLVERGKRLIDRGIPVLILGETGTGKEYLSRALHDYSARRRASWIAVNC 99 +QL M + ++ R VL+LGETGTGKE ++RALH AR ++AVNC Sbjct: 134 NQLVGESEAMRQVFKQIGRAATSDATVLVLGETGTGKELVARALHRNGARAARPFVAVNC 193 Query: 100 ASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVL 159 A+IP L ESELFG+ KGAFSGA + G+ Q+ADGGTLFLDEIGDM LA Q ++LRVL Sbjct: 194 AAIPAELIESELFGHVKGAFSGATSPRL-GRFQEADGGTLFLDEIGDMELATQAKILRVL 252 Query: 160 SEREVIPLGARHPVPVDVQLICATHQDLKTLIAEGRFREDLYYRVAGGVLRLPALRERSD 219 ERE+ P+G V VDV++I ATH+DL+ I +GRFREDL+YR+ + +PALRER Sbjct: 253 QERELTPVGGNQSVRVDVRVIAATHRDLQHEITQGRFREDLWYRLQVLTIMVPALRERPG 312 Query: 220 RRRLVMQMITEELGRSADDSVIEAAALQRLLAYPWPGNLRQMHAVIRYSCAVMNGGRIEV 279 + + +LG A + AAA + LL + WPGN+R++ + + + +G IE Sbjct: 313 DILTIAEHFLRQLGGDAPKRISPAAA-RLLLQHAWPGNVRELRNTMERAAVMSHGLCIEA 371 Query: 280 RDLPEELMQFQPATLAEVHPITRTAQIRPFTSRAEGEAGRERSSGDPYRDERTRVIDALN 339 D+ L PA A P A E ER + AL Sbjct: 372 EDIG--LSARPPAGAASAASAPAIDWDGPLAV-ALAEV------------ERVMIERALQ 416 Query: 340 GSRWNISAASRQLGMCRASLYRKLRQLDIPH 370 G+ N + A+R+LG+ R LYR+L + H Sbjct: 417 GAAGNRAEAARRLGISRQQLYRRLEEAGKSH 447 >gi|300312042|ref|YP_003776134.1| response regulatory protein [Herbaspirillum seropedicae SmR1] Length = 450 Score = 202 bits (515), Expect = 3e-53, Method: Compositional matrix adjust. Identities = 128/314 (40%), Positives = 180/314 (57%), Gaps = 47/314 (14%) Query: 66 VLILGETGTGKEYLSRALHDYSARRRASWIAVNCASIPESLAESELFGYCKGAFSGALPG 125 V++LG +GTGKE L+RALH S R ++A+NCA+IPE+L ESELFGY KGAF+GA Sbjct: 172 VMLLGSSGTGKEVLARALHQLSPRSGRRFMAINCAAIPENLLESELFGYEKGAFTGAAKQ 231 Query: 126 GMKGKVQQADGGTLFLDEIGDMPLALQTRLLRVLSEREVIPLGARHPVPVDVQLICATHQ 185 + GKV+ A GGT FLDE+GD+P+ LQ +LLR L ER + +G +PVDV++ICATHQ Sbjct: 232 TI-GKVELAHGGTFFLDEVGDLPMPLQAKLLRFLQERVIERVGGHTEIPVDVRVICATHQ 290 Query: 186 DLKTLIAEGRFREDLYYRVAGGVLRLPALRERSD-----RRRLVMQMITEELGRS----A 236 +LK L A G FREDLYYR+ ++++PAL+ER R V + +E GR+ + Sbjct: 291 NLKELTASGGFREDLYYRLCEIIIKIPALKERHGDAVLLARHFVQKFCAKE-GRATLHLS 349 Query: 237 DDSVIEAAALQRLLAYPWPGNLRQMHAVIRYSCAVMNGGRIEVRD--LPEELMQFQPATL 294 D+V AA++R Y WPGN+R+M + + + +G +I D L E + +P L Sbjct: 350 QDAV---AAIER---YEWPGNVREMENCVMRAVIMADGQQITAEDLGLSVEGREAEPLNL 403 Query: 295 AEVHPITRTAQIRPFTSRAEGEAGRERSSGDPYRDERTRVIDALNGSRWNISAASRQLGM 354 +V R E ER V+ AL NI A+ LG+ Sbjct: 404 RQV--------------RDEA--------------ERKAVVKALTRMDGNILKAAELLGV 435 Query: 355 CRASLYRKLRQLDI 368 R +LY + + +I Sbjct: 436 SRPTLYDLMSRHEI 449 >gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcription activator protein [Herbaspirillum seropedicae SmR1] Length = 500 Score = 197 bits (501), Expect = 1e-51, Method: Compositional matrix adjust. Identities = 116/266 (43%), Positives = 168/266 (63%), Gaps = 16/266 (6%) Query: 35 RYRDIDQLAA------GDA-CMHDLVERGKRLIDRGIPVLILGETGTGKEYLSRALHDYS 87 R DI+Q AA G A M D+ RL + VLI GE+G+GKE ++RALH +S Sbjct: 122 RETDIEQGAAQTPEILGQAPAMQDVFRAIGRLSQSNVTVLITGESGSGKELVARALHKHS 181 Query: 88 ARRRASWIAVNCASIPESLAESELFGYCKGAFSGALPGGMKGKVQQADGGTLFLDEIGDM 147 R ++A+N A+IP+ L ESELFG+ +GAF+GA +G+ +QA+GGTLFLDEIGDM Sbjct: 182 PRASQPFVALNTAAIPKDLLESELFGHERGAFTGA-QAMRRGRFEQAEGGTLFLDEIGDM 240 Query: 148 PLALQTRLLRVLSEREVIPLGARHPVPVDVQLICATHQDLKTLIAEGRFREDLYYRVAGG 207 PL LQTRLLRVLS+ +G + +V++I ATHQ+L+ + EG FREDLY+R+ Sbjct: 241 PLDLQTRLLRVLSDGHFYRVGGHQSLKANVRVIAATHQNLEQRVREGLFREDLYHRLNVI 300 Query: 208 VLRLPALRERSDRRRLVMQMITEELGRSADDSVIEAA-----ALQRLLAYPWPGNLRQMH 262 LRLP+LRERS+ ++ + L +SA +EA A+Q L +PGN+RQ+ Sbjct: 301 RLRLPSLRERSEDIPILARYF---LAQSARQLGVEAKRLSPQAMQFLSQLEFPGNVRQLE 357 Query: 263 AVIRYSCAVMNGGRIEVRDLPEELMQ 288 + + + G +E++DLP++L++ Sbjct: 358 NLCNWITVMAPGQTVEIKDLPQDLVE 383 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.320 0.135 0.397 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 1,220,364 Number of extensions: 52043 Number of successful extensions: 231 Number of sequences better than 1.0e-08: 12 Number of HSP's gapped: 205 Number of HSP's successfully gapped: 12 Length of query: 385 Length of database: 1,619,870 Length adjustment: 87 Effective length of query: 298 Effective length of database: 1,207,925 Effective search space: 359961650 Effective search space used: 359961650 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 131 (55.1 bits)